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<h2>Saving Your Work</h2>

The software provides a number of options available for saving your work.
These are detailed in the following sections.

<h3>Saving Everything</h3>
The most comprehensive approach for saving your work is available by
selecting the <tt>File->Save</tt> or <tt>File->Save As</tt> menu
options. These will save a P3D file with full details about the
reference molecule, pharmacophore (including your changes, if any),
and the contents of your Molecule Evaluation page.

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<h3>Exporting All Molecules</h3>
This command, accessible via the <tt>File->Export->All Evaluated Molecules</tt> menu
option, allows you to save an SD file containing all of the molecules
currently on the Molecule Evaluation page. 

<p>The molecules will be saved without information about 3D structure
or any mappings to the pharmacophore. A single copy of each molecule
will be saved, even if each has multiple mappings.

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<h3>Exporting Alignments</h3>
This command, accessible via the <tt>File->Export->Checked Alignments</tt> menu
option, allows you to save an SD file containing the aligned 3D
structures that are checked on the Molecule Evaluation page.

<p>If multiple alignments are selected for an individual molecule,
they will all be exported by this command.

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